75 Matching Annotations
  1. Nov 2022
    1. ChIP

      Workflow 1. Cross-linking 2. Chromatin fragmentation 3. Immunoprecipitation of chromatin 4. DNA recovery and purification 5. Sequencing of DNA

    2. analyze protein interactions

      ChIP-seq is concerned with testing for protein DNA interactions.

    1. When we expanded this analysis to chromosome-wide gene-gene correlations, we discovered a striking ‘X-shaped’ pattern of gene expression covariance (Fig. 1D). Beyond the expected diagonal reflecting coordinated gene expression at the level of operons, the anti-diagonal reflected correlations between genes at a similar distance from the origin of replication, between the “arms” of the circular chromosome, as well as a correlation between genes at the origin and terminus

      It would be really interesting to compare the patterns you observe here with the X-like genome inversion patterns that we and others have reported (e.g., see https://www.ncbi.nlm.nih.gov/pmc/articles/PMC16139/). These patterns basically show that the distance a gene is from the origin of replication is conserved but the side of the origin it is on is not.

      Those inversion patterns have been seen in some but not all comparisons of closely related bacterial and archaeal genomes. So it seems there are some taxa where the distance a gene is from the origin is not conserved over evolutionary time. It would be interesting to know if these taxa show the X-like patternb you report for gene expression.

  2. Oct 2022
  3. Jun 2022
    1. Among these, all VUS, variants with a zero-star reviewstatus, i.e., without any detailed review information, and those with conflicting classificationswere excluded

      dodgy labs might mark variant as pathogenic and link to assessment criteria but apply them wrongly. These might be detected if other labs post conflicting assessments. But for ultrarare variants, no other lab might have submitted that variant

  4. May 2022
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  8. Dec 2021
  9. Oct 2021
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  13. May 2021
    1. Faria, N. R., Mellan, T. A., Whittaker, C., Claro, I. M., Candido, D. da S., Mishra, S., Crispim, M. A. E., Sales, F. C. S., Hawryluk, I., McCrone, J. T., Hulswit, R. J. G., Franco, L. A. M., Ramundo, M. S., Jesus, J. G. de, Andrade, P. S., Coletti, T. M., Ferreira, G. M., Silva, C. A. M., Manuli, E. R., … Sabino, E. C. (2021). Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil. Science. https://doi.org/10.1126/science.abh2644

  14. Apr 2021
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  23. Nov 2017
    1. We do not have to worry about both bases in both strands. Any one strand is fine. Because A always pairs with T and C always pairs with G.

  24. Sep 2017
    1. The projection score - an evaluation criterion for variable subset selection in PCA visualization

      "variable" typically means gene or locus in the context of biological data.

  25. Apr 2017
    1. The Administration could also exercise its regulatory authority—most potently, to direct the Centers for Medicare and Medicaid Services (CMS) to allow reimbursement for molecular profiling of cancers

      Perhaps the most important measure to keep precision medicine initiate alive. Surge in risk and treatment response prediction in genomic assays is of little value without practical means of affordable molecular profiling of a patient's tumor or more importantly, pre-diagnosis genomic screen.

  26. Mar 2017
    1. Genome Sequence Archive (GSA)

      Database URL is here: http://gsa.big.ac.cn/

      Note: metadata is INSDC format, but this database isn't part of the INSDC, so you'll still need to submit your data to one of those databases to meet internationally recognised mandates

    1. The ENCODE portal is the official canonical source for ENCODE data and data from other related projects.

  27. Oct 2016
    1. blast

      BLAST finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance.

  28. Jun 2016
  29. Apr 2016
    1. Published in 2015

      These policies have been built on the Fort Lauderdale principles, see the original policies from 2003 https://www.genome.gov/10506537/

    1. Accession codes

      The panda and polar bear datasets should have been included in the data section rather than hidden in the URLs section. Production removed the DOIs and used (now dead) URLs instead, but for the working links and insight see the following blog: http://blogs.biomedcentral.com/gigablog/2012/12/21/promoting-datacitation-in-nature/

    1. Centralizing content and distributing labor: a community model for curating the very long tail of microbial genomes.

      This is going to be a good talk. Get your coffee, open your eyes, and open your mind! A pattern that could actually scale up - worth a try! Disagree? reply here.